On Thu, Feb 18, 2010, Dian Jiao wrote:
>
> I was running simulation with amoeba force field. It is a very small
> system ~2000 atoms.
>
> The first 2ns was done ok. But when I restarted the simulation after that,
> it kept dying due to "Too many dipole_dipole interactions for allocated".
> And everytime I restarted the job where it stopped, it would run for a while
> and then died again for the same reason. So in principle, I could continue
> the simulation to no matter how long I want but it just does not look right
> to me. What is causing that? Is it memory related?
Is the density changing during the run?
My suggestions, in order of preference:
1. use pmemd.amba, not sander. It is faster, better tested, and parallel to
boot.
2. try increasing the "safety" parameter in amoeba_direct.f in sander. The
code is trying to estimate how many intereactions will be needed, and it may
be making too conservative an estimate.
....dac
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Received on Thu Feb 18 2010 - 09:00:03 PST
